:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-biscuiteer' .. highlight: bash bioconductor-biscuiteer ======================= .. conda:recipe:: bioconductor-biscuiteer :replaces_section_title: :noindex: Convenience Functions for Biscuit :homepage: https://bioconductor.org/packages/3.18/bioc/html/biscuiteer.html :license: GPL-3 :recipe: /`bioconductor-biscuiteer `_/`meta.yaml `_ A test harness for bsseq loading of Biscuit output\, summarization of WGBS data over defined regions and in mappable samples\, with or without imputation\, dropping of mostly\-NA rows\, age estimates\, etc. .. conda:package:: bioconductor-biscuiteer |downloads_bioconductor-biscuiteer| |docker_bioconductor-biscuiteer| :versions: ``1.16.0-0``,  ``1.14.0-0``,  ``1.12.0-0``,  ``1.8.0-0``,  ``1.6.0-0``,  ``1.4.0-1``,  ``1.4.0-0``,  ``1.2.0-0``,  ``1.0.0-1`` :depends bioconductor-biobase: ``>=2.62.0,<2.63.0`` :depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0`` :depends bioconductor-biocparallel: ``>=1.36.0,<1.37.0`` :depends bioconductor-biscuiteerdata: ``>=1.16.0,<1.17.0`` :depends bioconductor-bsseq: ``>=1.38.0,<1.39.0`` :depends bioconductor-delayedmatrixstats: ``>=1.24.0,<1.25.0`` :depends bioconductor-dmrseq: ``>=1.22.0,<1.23.0`` :depends bioconductor-genomeinfodb: ``>=1.38.0,<1.39.0`` :depends bioconductor-genomicranges: ``>=1.54.0,<1.55.0`` :depends bioconductor-hdf5array: ``>=1.30.0,<1.31.0`` :depends bioconductor-homo.sapiens: ``>=1.3.0,<1.4.0`` :depends bioconductor-impute: ``>=1.76.0,<1.77.0`` :depends bioconductor-iranges: ``>=2.36.0,<2.37.0`` :depends bioconductor-mus.musculus: ``>=1.3.0,<1.4.0`` :depends bioconductor-qdnaseq: ``>=1.38.0,<1.39.0`` :depends bioconductor-rsamtools: ``>=2.18.0,<2.19.0`` :depends bioconductor-rtracklayer: ``>=1.62.0,<1.63.0`` :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0`` :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0`` :depends bioconductor-variantannotation: ``>=1.48.0,<1.49.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-data.table: :depends r-gtools: :depends r-matrix: :depends r-matrixstats: :depends r-qualv: :depends r-r.utils: :depends r-readr: :requirements: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `conda `_) and the Bioconda channel already activated (see :ref:`set-up-channels`). While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see `here `_ for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others. Given that you already have a conda environment in which you want to have this package, install with:: mamba install bioconductor-biscuiteer and update with:: mamba update bioconductor-biscuiteer To create a new environment, run:: mamba create --name myenvname bioconductor-biscuiteer with ``myenvname`` being a reasonable name for the environment (see e.g. the `mamba docs `_ for details and further options). Alternatively, use the docker container:: docker pull quay.io/biocontainers/bioconductor-biscuiteer: (see `bioconductor-biscuiteer/tags`_ for valid values for ````) .. |downloads_bioconductor-biscuiteer| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-biscuiteer.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-biscuiteer :alt: (downloads) .. |docker_bioconductor-biscuiteer| image:: https://quay.io/repository/biocontainers/bioconductor-biscuiteer/status :target: https://quay.io/repository/biocontainers/bioconductor-biscuiteer .. _`bioconductor-biscuiteer/tags`: https://quay.io/repository/biocontainers/bioconductor-biscuiteer?tab=tags .. raw:: html Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html Link to this page ----------------- Render an |install-with-bioconda| badge with the following MarkDown:: [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-biscuiteer/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/bioconductor-biscuiteer/README.html